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source: trunk/libIGCM/libIGCM_comp/libIGCM_comp.ksh @ 1645

Last change on this file since 1645 was 1645, checked in by aclsce, 4 months ago
Added modifications to run with no access to IDRIS STORE from computing nodes. Use of TMPSTORE to handle the writing/reading of restart files of running simulations. Use of OLDSTORE to handle reading of restart files of old simulations. The new STORE is only used from post-treatment jobs. Temporary solution waiting for the split of computing Job into pre-treatment job + computing Job.
Property licence set to The following licence information concerns ONLY the libIGCM tools ================================================================== Copyright © Centre National de la Recherche Scientifique CNRS Commissariat à l'Énergie Atomique CEA libIGCM : Library for Portable Models Computation of IGCM Group. IGCM Group is the french IPSL Global Climate Model Group. This library is a set of shell scripts and functions whose purpose is the management of the initialization, the launch, the transfer of output files, the post-processing and the monitoring of datas produce by any numerical program on any plateforme. This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info". As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors have only limited liability. In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the software by the user in light of its specific status of free software, that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions as regards security. The fact that you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms. Property svn:keywords set to `Revision Author Date`
File size: 87.8 KB

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1	#!/bin/ksh
2
3	#**************************************************************
4	# Author: Sebastien Denvil, Martial Mancip
5	# Contact: Sebastien.Denvil__at__ipsl.jussieu.fr Martial.Mancip__at__ipsl.jussieu.fr
6	# $Revision:: $ Revision of last commit
7	# $Author:: $ Author of last commit
8	# $Date:: $ Date of last commit
9	# IPSL (2006)
10	# This software is governed by the CeCILL licence see libIGCM/libIGCM_CeCILL.LIC
11	#
12	#**************************************************************
13
14	#========================================================================
15	function IGCM_comp_Initialize
16	{
17	IGCM_debug_PushStack "IGCM_comp_Initialize"
18
19	# Debug Print :
20	echo
21	IGCM_debug_Print 1 "IGCM_comp_Initialize"
22	echo
23
24	typeset comp compname comptagname auxprint card_UserChoices first_option option i j
25	for comp in ${config_ListOfComponents[*]} ; do
26
27	# Define component
28	IGCM_card_DefineArrayFromOption ${SUBMIT_DIR}/config.card ListOfComponents ${comp}
29	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
30	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
31
32	# Debug Print
33	IGCM_debug_Print 1 "Initialize ${comp} : ${compname} component."
34
35	# ${compname}.card PATH
36	card=${SUBMIT_DIR}/COMP/${compname}.card
37
38	# Manage component executable
39	IGCM_card_DefineArrayFromOption ${SUBMIT_DIR}/config.card Executable ${comp}
40
41	# Define all options in section [comp]
42	IGCM_debug_Print 3 " DefineArrayFromSection : ${comp}"
43	IGCM_card_DefineArrayFromSection ${SUBMIT_DIR}/config.card ${comp}
44	eval config_comp=\${config_${comp}[*]} > /dev/null 2>&1
45	for option in ${config_comp[*]} ; do
46	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} ${option}
47	done
48	IGCM_debug_Print 3 " Found in section config_${comp} : ${config_comp[*]} "
49
50	# Debug Print :
51	eval auxprint=\${config_${comp}_WriteFrequency}
52	IGCM_debug_Print 1 "Write frequency for ${compname} : ${auxprint} "
53	#2> /dev/null
54
55	# Debug Print :
56	IGCM_debug_Print 2 "Initialize following component library"
57
58	# Source drivers in directory DRIVER if it exist
59	# else source them from directory COMP
60	if [ -d ${SUBMIT_DIR}/DRIVER ] ; then
61	IGCM_debug_Print 2 ${SUBMIT_DIR}/DRIVER/${compname}.driver
62	# Source component library
63	. ${SUBMIT_DIR}/DRIVER/${compname}.driver
64	else
65	IGCM_debug_Print 2 ${SUBMIT_DIR}/COMP/${compname}.driver
66	# Source component library
67	. ${SUBMIT_DIR}/COMP/${compname}.driver
68	fi
69	IGCM_debug_Print 3 "With tag : ${comptagname}"
70
71	# Debug Print
72	IGCM_debug_Print 3 "Initialize ${comp} output directory."
73
74	# Define ARCHIVED Dirs
75	eval R_OUT_${comp}=${R_SAVE}/${comp}
76
77	eval R_OUT_${comp}_O=\${R_OUT_${comp}}/Output
78
79	eval R_OUT_${comp}_A=\${R_OUT_${comp}}/Analyse
80
81	eval R_OUT_${comp}_R=\${R_OUT_${comp}}/Restart
82	[ ${config_Post_PackFrequency} = NONE ] && eval IGCM_sys_MkdirArchive \${R_OUT_${comp}_R}
83
84	eval R_OUT_${comp}_D=\${R_OUT_${comp}}/Debug
85	[ ${config_Post_PackFrequency} = NONE ] && eval IGCM_sys_MkdirArchive \${R_OUT_${comp}_D}
86
87	eval R_OUT_${comp}_O_H=\${R_OUT_${comp}_O}/HF
88	eval R_OUT_${comp}_O_D=\${R_OUT_${comp}_O}/DA
89	eval R_OUT_${comp}_O_M=\${R_OUT_${comp}_O}/MO
90	eval R_OUT_${comp}_O_Y=\${R_OUT_${comp}_O}/YE
91
92	eval R_OUT_${comp}_A_H=\${R_OUT_${comp}_A}/TS_HF
93	eval R_OUT_${comp}_A_D=\${R_OUT_${comp}_A}/TS_DA
94	eval R_OUT_${comp}_A_M=\${R_OUT_${comp}_A}/TS_MO
95	eval R_OUT_${comp}_A_Y=\${R_OUT_${comp}_A}/TS_YE
96
97	# Define BUFFERED Dirs
98	if ( [ ! ${config_Post_PackFrequency} = NONE ] \|\| [ X${config_UserChoices_SpaceName} = XTEST ] ) ; then
99	eval R_BUF_${comp}=${R_BUFR}/${comp}
100	eval IGCM_sys_Mkdir \${R_BUF_${comp}}
101
102	eval R_BUF_${comp}_O=\${R_BUF_${comp}}/Output
103	eval IGCM_sys_Mkdir \${R_BUF_${comp}_O}
104
105	eval R_BUF_${comp}_A=\${R_BUF_${comp}}/Analyse
106	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A}
107
108	eval R_BUF_${comp}_R=\${R_BUF_${comp}}/Restart
109	eval IGCM_sys_Mkdir \${R_BUF_${comp}_R}
110
111	eval R_BUF_${comp}_D=\${R_BUF_${comp}}/Debug
112	eval IGCM_sys_Mkdir \${R_BUF_${comp}_D}
113
114	eval R_BUF_${comp}_O_H=\${R_BUF_${comp}_O}/HF
115	eval R_BUF_${comp}_O_D=\${R_BUF_${comp}_O}/DA
116	eval R_BUF_${comp}_O_M=\${R_BUF_${comp}_O}/MO
117	eval R_BUF_${comp}_O_Y=\${R_BUF_${comp}_O}/YE
118
119	eval R_BUF_${comp}_A_H=\${R_BUF_${comp}_A}/TS_HF
120	eval R_BUF_${comp}_A_D=\${R_BUF_${comp}_A}/TS_DA
121	eval R_BUF_${comp}_A_M=\${R_BUF_${comp}_A}/TS_MO
122	eval R_BUF_${comp}_A_Y=\${R_BUF_${comp}_A}/TS_YE
123
124	# Define CMIP6 Dirs
125	eval CMIP6_BUF_${comp}=${R_CMIP}/CMIP6/${comp}
126	fi
127
128	# Read UserChoices section of component card
129	IGCM_debug_Print 2 "DefineArrayFromSection : ${compname}_UserChoices ${card}"
130	IGCM_card_DefineArrayFromSection ${card} UserChoices
131	eval first_option=\${${compname}_UserChoices[0]} > /dev/null 2>&1
132
133	# If section is not empty we define corresponding variables
134	if [ X${first_option} != X"Error:" ] ; then
135	if [ X${card_UserChoices[0]} != X ] ; then
136	unset card_UserChoices
137	fi
138	eval set +A card_UserChoices -- \${${compname}_UserChoices[*]} > /dev/null 2>&1
139	IGCM_debug_Print 3 "${compname}_UserChoices_values:"
140	for option in ${card_UserChoices[*]} ; do
141	IGCM_card_DefineVariableFromOption ${card} UserChoices ${option}
142	eval IGCM_debug_Print 3 "${option}=\${${compname}_UserChoices_${option}}"
143	done
144	fi
145
146	# Read and Build Output File stuff
147	IGCM_debug_Print 2 "DefineArrayFromOption : ${compname}_OutputFiles ${card}"
148	IGCM_card_DefineArrayFromOption ${card} OutputFiles List
149	ListFilesName=${compname}_OutputFiles_List
150	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
151	#
152	if [ X${FileName0} != X${NULL_STR} ] ; then
153	#
154	#IGCM_debug_Print 1 "Component : ${compname}"
155	#
156	# INITIALISATION
157	#
158	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
159	#
160	i=2
161	#
162	until [ $i -ge $NbFiles ]; do
163	#
164	eval flag_post=\${${ListFilesName}[$i]} > /dev/null 2>&1
165	#
166	if [ X${flag_post} != XNONE ] ; then
167	#
168	# First of all
169	#
170	IGCM_card_DefineArrayFromSection ${card} ${flag_post}
171	# This section is mandatory
172	if [ "X$( eval echo \${${compname}_${flag_post}[@]} )" = "X" ] ; then
173	IGCM_debug_Print 1 "IGCM_card_DefineArrayFromSection ${card} ${flag_post}"
174	IGCM_debug_Exit "${flag_post} section do not exist in ${card}. Please check your card."
175	IGCM_debug_Verif_Exit
176	fi
177	#
178	# Seasonal case : If option Seasonal is not found (old cards) put SEASONAL ON by default
179	#
180	# variable option allready typeset above
181	for option in $( eval echo \${${compname}_${flag_post}[*]} ) ; do
182	if [ ${option} = Seasonal ] ; then
183	FoundSeasonal=true
184	IGCM_card_DefineVariableFromOption ${card} ${flag_post} Seasonal
185	fi
186	done
187	#
188	if [ ! X${FoundSeasonal} = Xtrue ] ; then
189	eval ${compname}_${flag_post}_Seasonal=ON
190	fi
191	#
192	if [ $( eval echo \${${compname}_${flag_post}_Seasonal} ) = ON ] ; then
193	Seasonal=true
194	fi
195
196	# Dimension = vide si vieille card.
197	IGCM_card_DefineArrayFromOption ${card} ${flag_post} TimeSeriesVars
198	IGCM_card_DefineArrayFromOption ${card} ${flag_post} Patches
199	if [ X"$( eval echo \${${compname}_${flag_post}_TimeSeriesVars[*]} )" = X"Option not" ] ; then
200	# New TimeSeriesVar description, with 2D, 3D and associate ChunckJob.
201	ListDimension[0]=2D
202	ListDimension[1]=3D
203	TimeSeries=false
204	iLoop=${#ListDimension[*]}
205	j=0
206	until [ $j -ge ${iLoop} ]; do
207	Dimension=${ListDimension[${j}]}
208	IGCM_card_DefineArrayFromOption ${card} ${flag_post} TimeSeriesVars${Dimension}
209	IGCM_card_DefineVariableFromOption ${card} ${flag_post} ChunckJob${Dimension}
210	#
211	# Time series WITHOUT chunk
212	#
213	if [ ! $( eval echo \${${compname}_${flag_post}_TimeSeriesVars${Dimension}} ) = ${NULL_STR} ] ; then
214	if [ $( eval echo \${${compname}_${flag_post}_ChunckJob${Dimension}} ) = NONE ] ; then
215	IGCM_debug_Print 3 "${Dimension} time series activated for ${flag_post}"
216	eval TimeSeries${Dimension}=true
217	fi
218	fi
219	#
220	# Time series WITH chunk
221	#
222	if [ ! $( eval echo \${${compname}_${flag_post}_TimeSeriesVars${Dimension}} ) = ${NULL_STR} ] ; then
223	chunck_size=$( eval echo \${${compname}_${flag_post}_ChunckJob${Dimension}} )
224	if [ ! ${chunck_size} = NONE ] && [ ! ${chunck_size} = OFF ] ; then
225	IGCM_debug_Print 3 "${Dimension} time series activated with chunck for ${flag_post}"
226	eval TimeSeriesChunck${Dimension}=true
227	eval CHUNCK${Dimension}_COMP[\${#CHUNCK${Dimension}_COMP[*]}]=${comp}
228	eval CHUNCK${Dimension}_FLAG[\${#CHUNCK${Dimension}_FLAG[*]}]=${i}
229	eval CHUNCK${Dimension}_NAME[\${#CHUNCK${Dimension}_NAME[*]}]=${flag_post}
230	eval CHUNCK${Dimension}_SIZE[\${#CHUNCK${Dimension}_SIZE[*]}]=${chunck_size}
231	fi
232	fi
233	(( j=j+1 ))
234	done
235	else
236	ListDimension[0]=""
237	TimeSeries=true
238	TimeSeries2D=false
239	TimeSeries3D=false
240	TimeSeriesChunck2D=false
241	TimeSeriesChunck3D=false
242	fi
243	fi
244	((i_ = i +1))
245	eval Testvar_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
246	eval Testvar=${Testvar_}
247	if [[ ${Testvar} =~ [0-9][DMY]$ ]] ; then
248	((i = i+4))
249	else
250	(( i=i+3 ))
251	fi
252	done
253	fi
254	# Debug Print
255	IGCM_debug_Print 3 "Initialize ${compname} with driver."
256	# INIT component
257	${comp}_Initialize
258	echo
259	done
260
261	IGCM_debug_PopStack "IGCM_comp_Initialize"
262	}
263
264	#=======================================================================
265	function IGCM_comp_PrepareDeletedFiles
266	{
267	IGCM_debug_PushStack "IGCM_comp_PrepareDeletedFiles" $@
268
269	if [ X${2} != X. ] ; then
270	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=$( basename ${2} ) > /dev/null 2>&1
271	else
272	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=$( basename ${1} ) > /dev/null 2>&1
273	fi
274
275	IGCM_debug_PopStack "IGCM_comp_PrepareDeletedFiles"
276	}
277
278	#=======================================================================
279	function IGCM_comp_PrepareXiosFiles
280	{
281	IGCM_debug_PushStack "IGCM_comp_PrepareXiosFiles" $@
282
283	typeset file
284	[ X${2} != X. ] && file=$( basename ${2} ) \|\| file=$( basename ${1} )
285
286	if [ $( echo ${file} \| grep "^field_def_" \| wc -l ) = 1 ] ; then
287	eval FieldDef[${#FieldDef[@]}]=${file} > /dev/null 2>&1
288	fi
289	if [ $( echo ${file} \| grep "^file_def_" \| wc -l ) = 1 ] ; then
290	eval FileDef[${#FileDef[@]}]=${file} > /dev/null 2>&1
291	fi
292	if [ $( echo ${file} \| grep "^timeseries_def_" \| wc -l ) = 1 ] ; then
293	eval FileDef[${#FileDef[@]}]=${file} > /dev/null 2>&1
294	fi
295
296	IGCM_debug_PopStack "IGCM_comp_PrepareXiosFiles"
297	}
298
299	#=======================================================================
300	function IGCM_comp_GetInputInitialStateFiles
301	{
302	IGCM_debug_PushStack "IGCM_comp_GetInputInitialStateFiles"
303
304	# Debug Print :
305	echo
306	IGCM_debug_Print 1 "IGCM_comp_GetInputInitialStateFiles"
307	echo
308
309	# Only the first time step need InitialStateFiles
310	# otherwise it's BoundaryConditions
311	if ( ${FirstInitialize} ) ; then
312	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
313	typeset file_in_ file_in file_out_ file_out do_init
314	for comp in ${config_ListOfComponents[*]} ; do
315	# Initialize
316	do_init="y"
317	# Do we need to bring initial state file for this component
318	if ( [ "${config_Restarts_OverRule}" = "y" ] \|\| [ "${config_Restarts_OverRule}" = "Y" ] ) ; then
319	eval do_init="n"
320	else
321	# Read component Restarts parameters
322	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} Restart
323	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
324	if [ "${do_start}" = "y" ] ; then
325	do_init="n"
326	else
327	do_init="y"
328	fi
329	fi
330
331	if [ "${do_init}" = "y" ] ; then
332	# Define component
333	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
334	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
335
336	# Debug Print :
337	IGCM_debug_Print 3 "Initialisation files ${compname}"
338
339	card=${SUBMIT_DIR}/COMP/${compname}.card
340
341	IGCM_card_DefineArrayFromOption ${card} InitialStateFiles List
342	ListFilesName=${compname}_InitialStateFiles_List
343
344	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
345	if [ X${FileName0} != X${NULL_STR} ] ; then
346	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
347	(( i=0 ))
348	until [ $i -ge $NbFiles ]; do
349	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
350	eval file_in=${file_in_}
351	(( i_ = i+1 ))
352	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
353	eval file_out=${file_out_}
354
355	IGCM_sys_IsFileArchived ${file_in}
356	if [ $? = 0 ] ; then
357	IGCM_sys_Get ${file_in} ${file_out}
358	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
359	else
360	IGCM_sys_Cp ${file_in} ${file_out}
361	fi
362	(( i=i+2 ))
363	done
364	fi
365	fi
366	done
367	fi
368	IGCM_debug_PopStack "IGCM_comp_GetInputInitialStateFiles"
369	}
370
371	#=======================================================================
372	# Definition of Smooth modulo function
373	# usage :
374	# IGCM_SmoothModulo StringModulo value
375	#
376	# StringModulo : A string of min max and modulo like definition of Scilab vectors.
377	# [min]:[modulo:][max]
378	# where :
379	# [] value are optionnals;
380	# empty min equal 1
381	# empty max equal infinity
382	# modulo not given or empty equal 1
383	# empty string or just ':' equal always.
384	#
385	# value : the value to test with the definition
386	#
387	# return : true(1)/false(0)
388	function IGCM_SmoothModulo
389	{
390	IGCM_debug_PushStack "IGCM_SmoothModulo"
391	typeset defVector ModValue
392
393	eval set +A defVector -- $( echo "${1}" \| \
394	gawk -F ':' '{print ($1 == "" ? 1 : $1) " " (NF==3 ? ($2 == "" ? 1 : $2) : 1) " " (NF==3 ? ($3 == "" ? -1 : $3) : ($2 == "" ? -1 : $2))}' )
395
396	# Save Smooth Min and Max. Needed to call IGCM_sys_Get when appropriate
397	arr[1]=${defVector[0]}
398	arr[2]=${defVector[2]}
399
400	# Test limits :
401	# ${defVector[0]} <= ${2} <= ${defVector[2]}
402	# or ${defVector[2]} == -1
403	if ( [ ${2} -ge ${defVector[0]} ] && ( [ ${2} -le ${defVector[2]} ] \|\| [ ${defVector[2]} -lt 0 ] ) ) ; then
404	# Test modulo
405	ModValue=$( expr \( ${2} - ${defVector[0]} \) % ${defVector[1]} )
406	if [ ${ModValue} -eq 0 ] ; then
407	arr[3]=true
408	echo ${arr[@]}
409	IGCM_debug_PopStack "IGCM_SmoothModulo"
410	return 1
411	else
412	arr[3]=false
413	echo ${arr[@]}
414	IGCM_debug_PopStack "IGCM_SmoothModulo"
415	return 0
416	fi
417	else
418	arr[3]=false
419	echo ${arr[@]}
420	IGCM_debug_PopStack "IGCM_SmoothModulo"
421	return 0
422	fi
423	}
424
425	#=======================================================================
426	function IGCM_comp_GetInputSmoothFiles
427	{
428	IGCM_debug_PushStack "IGCM_comp_GetInputSmoothFiles"
429
430	# Debug Print :
431	echo
432	IGCM_debug_Print 1 "IGCM_comp_GetInputSmoothFiles"
433	echo
434
435	typeset comp compname comptagname card ListFilesName FileName0 NbFiles j i i_ i__
436	typeset file_in_ file_in file_out_ file_out ret SmoothDef aux val
437
438	for comp in ${config_ListOfComponents[*]} ; do
439	# Define component
440	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
441	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
442
443	# Debug Print :
444	IGCM_debug_Print 3 "Smooth files ${compname}"
445
446	card=${SUBMIT_DIR}/COMP/${compname}.card
447
448	IGCM_card_DefineArrayFromOption ${card} SmoothFiles List
449	ListFilesName=${compname}_SmoothFiles_List
450	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
451
452	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != X"Section" ] ) ; then
453	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
454
455	(( i=0 ))
456	until [ $i -ge $NbFiles ]; do
457	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
458	eval file_in=${file_in_}
459	(( i_ = i+1 ))
460	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
461	eval file_out=${file_out_}
462
463	# define CumulPeriod definition for this file
464	(( i__ = i+2 ))
465	eval SmoothDef=\${${ListFilesName}[$i__]}
466	IGCM_debug_Print 3 " ${file_in} ${SmoothDef}"
467	aux=$( IGCM_SmoothModulo ${SmoothDef} ${CumulPeriod} )
468	j=1
469	for val in ${aux} ; do
470	[ ${j} -eq 1 ] && SmoothMin=${val}
471	[ ${j} -eq 2 ] && SmoothMax=${val}
472	[ ${j} -eq 3 ] && ret=${val}
473	(( j=j+1 ))
474	done
475	[ ${SmoothMax} -eq -1 ] && SmoothMax=${CumulPeriod}
476	if ( [ X${ret} = Xtrue ] \|\| ( [ ${Period} -eq 1 ] && [ ${CumulPeriod} -ge ${SmoothMin} ] && [ ${CumulPeriod} -le ${SmoothMax} ] ) ) ; then
477
478	IGCM_sys_IsFileArchived ${file_in}
479	if [ $? = 0 ] ; then
480	IGCM_sys_Get ${file_in} ${file_out}
481	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
482	else
483	IGCM_sys_Cp ${file_in} ${file_out}
484	fi
485	fi
486	(( i=i+3 ))
487	done
488	fi
489	done
490
491	IGCM_debug_PopStack "IGCM_comp_GetInputSmoothFiles"
492	}
493
494	#=======================================================================
495	function IGCM_comp_GetInputBoundaryFiles
496	{
497	IGCM_debug_PushStack "IGCM_comp_GetInputBoundaryFiles"
498
499	# Debug Print :
500	echo
501	IGCM_debug_Print 1 "IGCM_comp_GetInputBoundaryFiles"
502	echo
503
504	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
505	typeset file_in_ file_in file_out_ file_out
506
507	if [ ${Period} = 1 ]; then
508	ListFixBoundary=" "
509	fi
510
511	for comp in ${config_ListOfComponents[*]} ; do
512
513	# Define component
514	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
515	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
516
517	# Debug Print :
518	IGCM_debug_Print 3 "Boundary files ${compname}"
519
520	card=${SUBMIT_DIR}/COMP/${compname}.card
521
522	IGCM_card_DefineArrayFromOption ${card} BoundaryFiles List
523	ListFilesName=${compname}_BoundaryFiles_List
524	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
525
526	if [ X${FileName0} != X${NULL_STR} ] ; then
527	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
528
529	(( i=0 ))
530	until [ $i -ge $NbFiles ]; do
531	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
532	eval file_in=${file_in_}
533	(( i_ = i+1 ))
534	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
535	eval file_out=${file_out_}
536
537	IGCM_sys_IsFileArchived ${file_in}
538	if [ $? = 0 ] ; then
539	IGCM_sys_Get ${file_in} ${file_out}
540	IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
541	else
542	IGCM_sys_Cp ${file_in} ${file_out}
543	fi
544
545	(( i=i+2 ))
546	done
547	fi
548
549	# Get non deleted files
550	if [ ${Period} = 1 ]; then
551
552	IGCM_card_DefineArrayFromOption ${card} BoundaryFiles ListNonDel
553	ListFilesName=${compname}_BoundaryFiles_ListNonDel
554	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
555
556	if [ X${FileName0} != X${NULL_STR} ] ; then
557	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
558
559	(( i=0 ))
560	until [ $i -ge $NbFiles ]; do
561	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
562	eval file_in=${file_in_}
563	(( i_ = i+1 ))
564	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
565	eval file_out=${file_out_}
566
567	IGCM_sys_IsFileArchived ${file_in}
568	if [ $? = 0 ] ; then
569	IGCM_sys_Get ${file_in} ${file_out}
570	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
571	else
572	IGCM_sys_Cp ${file_in} ${file_out}
573	fi
574
575	if [ X${file_out} != X. ] ; then
576	ListFixBoundary=${ListFixBoundary}" "${file_out}
577	else
578	ListFixBoundary=${ListFixBoundary}" "$( basename ${file_in} )
579	fi
580
581	(( i=i+2 ))
582	done
583	fi
584	fi
585	done
586
587	IGCM_debug_PopStack "IGCM_comp_GetInputBoundaryFiles"
588	}
589
590	#=======================================================================
591	function IGCM_comp_DelFixeBoundaryFiles
592	{
593	IGCM_debug_PushStack "IGCM_comp_DelFixeBoundaryFiles"
594
595	# Debug Print :
596	echo
597	IGCM_debug_Print 1 "IGCM_comp_DelFixeBoundaryFiles"
598	echo
599
600	ls -l ${ListFixBoundary}
601	rm -f ${ListFixBoundary}
602
603	IGCM_debug_PopStack "IGCM_comp_DelFixeBoundaryFiles"
604	}
605
606	#=======================================================================
607	function IGCM_comp_GetInputParametersFiles
608	{
609	IGCM_debug_PushStack "IGCM_comp_GetInputParametersFiles"
610
611	# Debug Print :
612	echo
613	IGCM_debug_Print 1 "IGCM_comp_GetInputParametersFiles"
614	echo
615
616	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_ file_in file_out
617	for comp in ${config_ListOfComponents[*]} ; do
618	# Define component
619	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
620	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
621
622	# Initialize array hosting file_def and field_def files to check and/or modify
623	unset FieldDef
624	unset FileDef
625
626	# Debug Print :
627	IGCM_debug_Print 3 "Parameters ${compname}"
628
629	card=${SUBMIT_DIR}/COMP/${compname}.card
630
631	IGCM_card_DefineArrayFromOption ${card} ParametersFiles List
632	ListFilesName=${compname}_ParametersFiles_List
633	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
634
635	if [ X${FileName0} != X${NULL_STR} ] ; then
636	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
637
638	(( i=0 ))
639	until [ $i -ge $NbFiles ]; do
640	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
641	eval file_in=${file_in_}
642	(( i_ = i+1 ))
643	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
644	eval file_out=${file_out_}
645
646	IGCM_sys_Cp ${file_in} ${file_out}
647	IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
648	IGCM_comp_PrepareXiosFiles ${file_in} ${file_out}
649
650	(( i=i+2 ))
651	done
652	fi
653
654	done
655
656	IGCM_debug_PopStack "IGCM_comp_GetInputParametersFiles"
657	}
658
659	#=======================================================================
660	function IGCM_comp_GetInputRestartFiles
661	{
662	IGCM_debug_PushStack "IGCM_comp_GetInputRestartFiles"
663
664	# Debug Print :
665	echo
666	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles"
667	echo
668
669	typeset Date_tmp Date_r Path_r do_start CompOldName Path_OUT Path_BUF
670	typeset Buffered Archived Tared PotentialTarFile IsMatching TarFileFound
671	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
672	typeset file_in file_out file_in_ file_out_ file_in_Name
673	typeset -Z4 j4
674	#BASH declare j4
675
676	IsMatching=""
677
678	for comp in ${config_ListOfComponents[*]} ; do
679	# Define component
680	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
681	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
682	#
683	card=${SUBMIT_DIR}/COMP/${compname}.card
684	#
685	IGCM_card_DefineArrayFromOption ${card} RestartFiles List
686	ListFilesName=${compname}_RestartFiles_List
687	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
688
689	# Debug Print :
690	IGCM_debug_Print 3 "restart ${compname}"
691
692	if ( ${FirstInitialize} ) ; then
693
694	if ( [ "${config_Restarts_OverRule}" = "y" ] \|\| [ "${config_Restarts_OverRule}" = "Y" ] ) ; then
695	# Adhoc exception for CMIP6 : exclude XIOS from the restart overrule mechanism.
696	if ( [ X${comp} = XIOS ] ) && ( [ X"$( echo ${config_UserChoices_ExpType} \| grep CMIP6 )" != "X" ] \|\| [ X${config_Post_dr2xmlIPSL} = XTRUE ] ) ; then
697	CompOldName=IOS
698	config_IOS_Restart="n"
699	do_start="n"
700	config_IOS_RestartDate=-1
701	config_IOS_RestartJobName=${NULL_STR}
702	config_IOS_RestartPath=${NULL_STR}
703	else
704	eval config_${comp}_Restart="y"
705	eval config_${comp}_RestartDate=${config_Restarts_RestartDate}
706	eval config_${comp}_RestartJobName=${config_Restarts_RestartJobName}
707	eval config_${comp}_RestartPath=${config_Restarts_RestartPath}
708	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
709	eval CompOldName=${comp}
710	fi
711	else
712	# Read component Restarts parameters
713	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} Restart
714	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
715
716	if [ "${do_start}" = "y" ] ; then
717	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartDate
718	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartJobName
719	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartPath
720	else
721	eval config_${comp}_RestartDate=-1
722	eval config_${comp}_RestartJobName=${NULL_STR}
723	eval config_${comp}_RestartPath=${NULL_STR}
724	fi
725
726	eval CompOldName=\${config_${comp}_OldName}
727	if [ X${CompOldName} = X ] ; then
728	eval CompOldName=${comp}
729	fi
730
731	# Reinitialize IsMatching to allow searching for a different tar file for each component.
732	IsMatching=""
733	TarFileFound=""
734	fi
735
736	if [ "${do_start}" = "y" ] ; then
737
738	# Restore Restarts files
739	#-----------------------
740	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
741	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
742
743	(( i=1 ))
744	until [ $i -gt $NbFiles ]; do
745	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
746	eval file_in=${file_in_}
747	(( i_ = i+1 ))
748	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
749	eval file_out=${file_out_}
750
751	(( i_ = i+2 ))
752	eval is_opt=\${${ListFilesName}[$i_]} > /dev/null 2>&1
753	if [ X${is_opt} = XOPTIONAL ] ; then
754	echo ${file_in} is optional
755	(( i=i+4 ))
756	else
757	is_opt="MANDATORY"
758	echo ${file_in} is mandatory
759	(( i=i+3 ))
760	fi
761	IGCM_debug_Print 3 "Now search for restart file ${file_in} which is ${is_opt} (in section do_start=y)"
762
763	eval Date_tmp=\${config_${comp}_RestartDate}
764	Date_r=$( IGCM_date_ConvertFormatToGregorian ${Date_tmp} )
765	# will be re-use
766	eval RestartPath=\${config_${comp}_RestartPath}
767	eval RestartJobName=\${config_${comp}_RestartJobName}
768	#
769	Path_r=${RestartPath}/${RestartJobName}/${CompOldName}/Restart
770	file_in_Name=${RestartJobName}_${Date_r}_${file_in}
771
772	extension_in=$( echo ${file_in_Name##*.} )
773	extension_out=$( echo ${file_out##*.} )
774
775	generic_restart_file_name_in=$( basename ${file_in_Name} .${extension_in} )
776	generic_restart_file_name_out=$( basename ${file_out} .${extension_out} )
777
778	Path_OUT=${Path_r}/${generic_restart_file_name_in}
779
780	if [ ! X${OLDARCHIVE} = X ]; then
781	IsSTOREFlag=$( [ X$( echo ${Path_OUT} \| grep fsstor ) != X ] && echo 0 \|\| echo 1 )
782	if [ ${IsSTOREFlag} = 0 ] ; then
783	Path_OLDOUT=$( echo ${Path_OUT} \| sed "s%/lustre/fsstor/projects%/gpfsstore%" )
784	else
785	Path_OLDOUT="null"
786	fi
787	fi
788
789	if [ ! X${TMPARCHIVE} = X ]; then
790	IsSTOREFlag=$( [ X$( echo ${Path_OUT} \| grep fsstor ) != X ] && echo 0 \|\| echo 1 )
791	if [ ${IsSTOREFlag} = 0 ] ; then
792	Path_TMPOUT=$( echo ${Path_OUT} \| sed "s%/lustre/fsstor/projects%/lustre/fsnomig/ipsl/tmpstore%" )
793	else
794	Path_TMPOUT="null"
795	fi
796	fi
797
798	if [ $( IGCM_sys_TestFileBuffer ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
799	IGCM_debug_Print 3 "Buffered restart ${Path_OUT}*.${extension_in} "
800	Buffered=true
801	Archived=false
802	Tared=false
803	nb_restart_file=$(IGCM_sys_CountFileBuffer ${Path_OUT}_????.${extension_in})
804	elif [ $( IGCM_sys_TestFileArchive ${Path_OLDOUT}*.${extension_in} ; echo $? ) = 0 ] ; then
805	IGCM_debug_Print 3 "Archived restart ${Path_OLDOUT}*.${extension_in}"
806	Buffered=false
807	Archived=true
808	Tared=false
809	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_OLDOUT}_????.${extension_in})
810	Path_OUT=${Path_OLDOUT}
811	elif [ $( IGCM_sys_TestFileArchive ${Path_TMPOUT}*.${extension_in} ; echo $? ) = 0 ] ; then
812	IGCM_debug_Print 3 "Archived restart ${Path_TMPOUT}*.${extension_in}"
813	Buffered=false
814	Archived=true
815	Tared=false
816	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_TMPOUT}_????.${extension_in})
817	Path_OUT=${Path_TMPOUT}
818	elif [ $( IGCM_sys_TestFileArchive ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
819	IGCM_debug_Print 3 "Archived restart ${Path_OUT}*.${extension_in}"
820	Buffered=false
821	Archived=true
822	Tared=false
823	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_OUT}_????.${extension_in})
824	else
825	IGCM_debug_Print 3 "No restart file in the buffer nor in the archive directory"
826	IGCM_debug_Print 3 "${Path_OUT}*.${extension_in} do not exist"
827	IGCM_debug_Print 3 "Restart files will now be searched for in : ${RestartPath}/${RestartJobName}/RESTART"
828	Buffered=false
829	Archived=false
830	Tared=true
831	# Look after the tar file we want if we did not found it already
832	if [ X${IsMatching} = X ] ; then
833	if ( [ ! X${OLDARCHIVE} = X ] && [ ! X${TMPARCHIVE} = X ] ) ; then
834	IsSTOREFlag=$( [ X$( echo ${RestartPath} \| grep fsstor ) != X ] && echo 0 \|\| echo 1 )
835	if [ ${IsSTOREFlag} = 0 ] ; then
836	OLDRestartPath=$( echo ${RestartPath} \| sed "s%/lustre/fsstor/projects%/gpfsstore%" )
837	TMPRestartPath=$( echo ${RestartPath} \| sed "s%/lustre/fsstor/projects%/lustre/fsnomig/ipsl/tmpstore%" )
838	else
839	OLDRestartPath="null"
840	TMPRestartPath="null"
841	fi
842	IGCM_sys_TestDirArchive ${OLDRestartPath}/${RestartJobName}/RESTART
843	if [ $? = 0 ] ; then
844	RestartPath=${OLDRestartPath}
845	else
846	IGCM_sys_TestDirArchive ${TMPRestartPath}/${RestartJobName}/RESTART
847	if [ $? = 0 ] ; then
848	RestartPath=${TMPRestartPath}
849	fi
850	fi
851	fi
852	IGCM_sys_TestDirArchive ${RestartPath}/${RestartJobName}/RESTART
853	if [ $? ] ; then
854	for PotentialTarFile in $( IGCM_sys_RshArchive "find ${RestartPath}/${RestartJobName}/RESTART -name "${RestartJobName}_restart.tar" -print" ) ; do
855	IsMatching=$( echo ${PotentialTarFile##*/} \| \
856	sed "s:_restart::" \| \
857	sed "s:^${RestartJobName}_::" \| \
858	sed "s:\.tar$::" \| \
859	gawk -F_ -v restartdate=${Date_r} \
860	'{if (($1 <= restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
861	if [ ! X${IsMatching} = X ] ; then
862	TarFileFound=${PotentialTarFile}
863	break
864	fi
865	done
866	fi
867
868	# Stop here if nothing has been found
869	if [ X${TarFileFound} = X ] ; then
870	IGCM_debug_Print 3 "Restart files were not found!"
871	IGCM_debug_Print 3 "Restart files have been searched for in buffer and archive directory."
872	IGCM_debug_Print 3 "They have been searched for in packed and unpacked format."
873	if [ ${is_opt} = 'OPTIONAL' ] ; then
874	IGCM_debug_Print 3 "The restart file is optional. Now continue."
875	nb_restart_file=0
876	Tared=false
877	else
878	IGCM_debug_Exit "Please double check restart settings in config.card"
879	IGCM_debug_Verif_Exit
880	fi
881	fi
882	fi
883
884	if [ X${Tared} = Xtrue ] ; then
885	# The tar file exist but not sure all files are inside
886	IGCM_sys_PrepareTaredRestart ${TarFileFound}
887	TarFileLocation=$( basename ${TarFileFound} )
888	nb_files=$( tar tvf ${TarFileLocation} \| grep ${comp}_${generic_restart_file_name_in} \| wc -l )
889	if [ ${nb_files} -gt 0 ] ; then
890	IGCM_debug_Print 1 "tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}"
891	tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}
892	nb_restart_file=$( IGCM_sys_CountFileBuffer ${comp}_${generic_restart_file_name_in}_????.${extension_in} )
893	else
894	# No file was found
895	if [ ${is_opt} = 'OPTIONAL' ] ; then
896	IGCM_debug_Print 3 "The restart file is not found in the tar file but it is optional. Now continue."
897	nb_restart_file=0
898	Tared=false
899	else
900	IGCM_debug_Print 3 "The restart file was not found in the tar file but it is mandatory."
901	IGCM_debug_Exit "Please double check restart settings in config.card"
902	IGCM_debug_Verif_Exit
903	fi
904	fi
905	fi
906	fi
907
908	if [ ${nb_restart_file} -gt 1 ] ; then
909	j=0 # BASH LINE NOT NEEDED
910	# BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
911	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
912	j4=${j} # BASH LINE NOT NEEDED
913	if [ X${Buffered} = Xtrue ] ; then
914	IGCM_sys_GetBuffer ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
915	elif [ X${Archived} = Xtrue ] ; then
916	IGCM_sys_Get ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
917	elif [ X${Tared} = Xtrue ] ; then
918	IGCM_sys_Mv ${comp}_${generic_restart_file_name_in}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
919	fi
920	(( j=j+1 )) #BASH LINE NOT NEEDED
921	done
922
923	# OCE SPECIFIC TO REBUILD RESTART WHEN NUMBER OF RESTART FILES DONT MATCH MPI PROCESS
924	if [ X${OCE_PROC_MPI} != X ] ; then
925	if [ ${OCE_PROC_MPI} -ne ${nb_restart_file} ] ; then
926	IGCM_sys_rebuild_nemo ${generic_restart_file_name_out} ${nb_restart_file} ${extension_out} ${generic_restart_file_name_out}_????.${extension_out}
927	IGCM_sys_Rm ${generic_restart_file_name_out}_????.${extension_out}
928	fi
929	fi
930	else
931	if [ X${Buffered} = Xtrue ] ; then
932	IGCM_sys_GetBuffer ${Path_r}/${file_in_Name} ${file_out}
933	elif [ X${Archived} = Xtrue ] ; then
934	IGCM_sys_Get ${Path_r}/${file_in_Name} ${file_out}
935	elif [ X${Tared} = Xtrue ] ; then
936	if [ -f ${comp}_${file_in_Name} ] ; then
937	# The file exixt
938	IGCM_sys_Mv ${comp}_${file_in_Name} ${file_out}
939	elif [ ${is_opt} = 'OPTIONAL' ] ; then
940	IGCM_debug_Print 3 "The restart file is not found in the tar file but it is optional. Now continue."
941	else
942	IGCM_debug_Print 3 "The restart file was not found in the tar file but it is mandatory."
943	IGCM_debug_Exit "Please double check restart settings in config.card"
944	IGCM_debug_Verif_Exit
945	fi
946	fi
947	fi
948	done
949	else
950	if [ X${FileName0} != XNONE ] ; then
951	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
952	else
953	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
954	fi
955	fi
956	fi
957	elif ( [ ${Period} -eq 1 ] && [ ${DRYRUN} -eq 0 ] ) ; then
958	# if not FirstInitialize and first loop of this job
959
960	# Restore Restarts files
961	#-----------------------
962	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
963	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
964
965	(( i=1 ))
966	until [ $i -gt $NbFiles ]; do
967	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
968	eval file_in=${file_in_}
969
970	(( i_ = i+1 ))
971	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
972	eval file_out=${file_out_}
973
974	(( i_ = i+2 ))
975	eval is_opt=\${${ListFilesName}[$i_]} > /dev/null 2>&1
976	if [ X${is_opt} = XOPTIONAL ] ; then
977	# Read a forth argument
978	echo ${file_in} is optional
979	(( i=i+4 ))
980	else
981	is_opt="MANDATORY"
982	echo ${file_in} is mandatory
983	(( i=i+3 ))
984	fi
985
986	IGCM_debug_Print 3 "Now search for restart file ${file_in} which is ${is_opt} (in section do_start=n)"
987
988	file_in_Name=${config_UserChoices_JobName}_${LastPeriodDateEnd}_${file_in}
989
990	extension_in=$( echo ${file_in_Name##*.} )
991	extension_out=$( echo ${file_out##*.} )
992
993	generic_restart_file_name_in=$( basename ${file_in_Name} .${extension_in} )
994	generic_restart_file_name_out=$( basename ${file_out} .${extension_out} )
995
996	eval Path_BUF=\${R_BUF_${comp}_R}/${generic_restart_file_name_in}
997	eval Path_OUT=\${R_OUT_${comp}_R}/${generic_restart_file_name_in}
998
999	if [ ! X${OLDARCHIVE} = X ]; then
1000	IsSTOREFlag=$( [ X$( echo ${Path_OUT} \| grep fsstor ) != X ] && echo 0 \|\| echo 1 )
1001	if [ ${IsSTOREFlag} = 0 ] ; then
1002	Path_OLDOUT=$( echo ${Path_OUT} \| sed "s%/lustre/fsstor/projects%/gpfsstore%" )
1003	else
1004	Path_OLDOUT="null"
1005	fi
1006	fi
1007
1008	if [ ! X${TMPARCHIVE} = X ]; then
1009	IsSTOREFlag=$( [ X$( echo ${Path_OUT} \| grep fsstor ) != X ] && echo 0 \|\| echo 1 )
1010	if [ ${IsSTOREFlag} = 0 ] ; then
1011	Path_TMPOUT=$( echo ${Path_OUT} \| sed "s%/lustre/fsstor/projects%/lustre/fsnomig/ipsl/tmpstore%" )
1012	else
1013	Path_TMPOUT="null"
1014	fi
1015	fi
1016	if [ $( IGCM_sys_TestFileBuffer ${Path_BUF}*.${extension_in} ; echo $? ) = 0 ] ; then
1017	IGCM_debug_Print 3 "Buffered restart ${Path_BUF}*.${extension_in}"
1018	Buffered=true
1019	Archived=false
1020	Tared=false
1021	nb_restart_file=$(IGCM_sys_CountFileBuffer ${Path_BUF}_????.${extension_in})
1022	elif [ $( IGCM_sys_TestFileArchive ${Path_OLDOUT}*.${extension_in} ; echo $? ) = 0 ] ; then
1023	IGCM_debug_Print 3 "Archived restart ${Path_OLDOUT}*.${extension_in}"
1024	Buffered=false
1025	Archived=true
1026	Tared=false
1027	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_OLDOUT}_????.${extension_in})
1028	Path_OUT=${Path_OLDOUT}
1029	elif [ $( IGCM_sys_TestFileArchive ${Path_TMPOUT}*.${extension_in} ; echo $? ) = 0 ] ; then
1030	IGCM_debug_Print 3 "Archived restart ${Path_TMPOUT}*.${extension_in}"
1031	Buffered=false
1032	Archived=true
1033	Tared=false
1034	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_TMPOUT}_????.${extension_in})
1035	Path_OUT=${Path_TMPOUT}
1036	elif [ $( IGCM_sys_TestFileArchive ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
1037	IGCM_debug_Print 3 "Archived restart ${Path_OUT}*.${extension_in}"
1038	Buffered=false
1039	Archived=true
1040	Tared=false
1041	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_OUT}_????.${extension_in})
1042	else
1043	IGCM_debug_Print 3 "No restart file in the buffer nor in the archive directory"
1044	IGCM_debug_Print 3 "Restart files will now be searched for in : ${R_SAVE}/RESTART"
1045	Buffered=false
1046	Archived=false
1047	Tared=true
1048	# Look after the tar file we want if we did not found it already
1049	if [ X${IsMatching} = X ] ; then
1050	if ( [ ! X${OLDARCHIVE} = X ] && [ ! X${TMPARCHIVE} = X ] ) ; then
1051	for PotentialTarFile in $( IGCM_sys_RshArchive "find ${R_OLDSAVE}/RESTART -name "${config_UserChoices_JobName}_*_restart.tar" -print" ) ; do
1052	IsMatching=$( echo ${PotentialTarFile##*/} \| sed "s:^${config_UserChoices_JobName}_::" \| sed "s:\.restart\.tar$::" \| gawk -F_ -v restartdate=${LastPeriodDateEnd} '{if (($1 < restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
1053	if [ ! X${IsMatching} = X ] ; then
1054	TarFileFound=${PotentialTarFile}
1055	break
1056	else
1057	for PotentialTarFile in $( IGCM_sys_RshArchive "find ${R_TMPSAVE}/RESTART -name "${config_UserChoices_JobName}_*_restart.tar" -print" ) ; do
1058	IsMatching=$( echo ${PotentialTarFile##*/} \| sed "s:^${config_UserChoices_JobName}_::" \| sed "s:\.restart\.tar$::" \| gawk -F_ -v restartdate=${LastPeriodDateEnd} '{if (($1 < restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
1059	if [ ! X${IsMatching} = X ] ; then
1060	TarFileFound=${PotentialTarFile}
1061	break
1062	else
1063	for PotentialTarFile in $( IGCM_sys_RshArchive "find ${R_SAVE}/RESTART -name "${config_UserChoices_JobName}_*_restart.tar" -print" ) ; do
1064	IsMatching=$( echo ${PotentialTarFile##*/} \| sed "s:^${config_UserChoices_JobName}_::" \| sed "s:\.restart\.tar$::" \| gawk -F_ -v restartdate=${LastPeriodDateEnd} '{if (($1 < restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
1065	if [ ! X${IsMatching} = X ] ; then
1066	TarFileFound=${PotentialTarFile}
1067	break
1068	fi
1069	done
1070	fi
1071	done
1072	fi
1073	done
1074	else
1075	for PotentialTarFile in $( IGCM_sys_RshArchive "find ${R_SAVE}/RESTART -name "${config_UserChoices_JobName}_*_restart.tar" -print" ) ; do
1076	IsMatching=$( echo ${PotentialTarFile##*/} \| sed "s:^${config_UserChoices_JobName}_::" \| sed "s:\.restart\.tar$::" \| gawk -F_ -v restartdate=${LastPeriodDateEnd} '{if (($1 < restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
1077	if [ ! X${IsMatching} = X ] ; then
1078	TarFileFound=${PotentialTarFile}
1079	break
1080	fi
1081	done
1082	fi
1083	fi
1084
1085	# Stop here if nothing has been found
1086	if [ X${TarFileFound} = X ] ; then
1087	IGCM_debug_Print 3 "Restart files were not found!"
1088	IGCM_debug_Print 3 "Restart files have been searched for in buffer and archive directory."
1089	IGCM_debug_Print 3 "They have been searched for in packed and unpacked format."
1090	if [ ${is_opt} = 'OPTIONAL' ] ; then
1091	IGCM_debug_Print 3 "The restart file is optional. Now continue."
1092	nb_restart_file=0
1093	Tared=false
1094	else
1095	IGCM_debug_Print 3 "The restart file is mandatory."
1096	IGCM_debug_Exit "Please double check restart settings in config.card"
1097	IGCM_debug_Verif_Exit
1098	fi
1099	else
1100	# The tar file exist but not sure all files are inside
1101	IGCM_sys_PrepareTaredRestart ${TarFileFound}
1102	TarFileLocation=$( basename ${TarFileFound} )
1103	nb_files=$( tar tvf ${TarFileLocation} \| grep ${comp}_${generic_restart_file_name_in} \| wc -l )
1104	if [ ${nb_files} -gt 0 ] ; then
1105	IGCM_debug_Print 1 "tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}"
1106	tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}
1107	nb_restart_file=$( IGCM_sys_CountFileBuffer ${comp}_${generic_restart_file_name_in}_????.${extension_in} )
1108	else
1109	# No file was found
1110	if [ ${is_opt} = 'OPTIONAL' ] ; then
1111	IGCM_debug_Print 3 "The restart file is not found in the tar file but it is optional. Now continue."
1112	nb_restart_file=0
1113	Tared=false
1114	else
1115	IGCM_debug_Print 3 "The restart file was not found in the tar file but it is mandatory."
1116	IGCM_debug_Exit "Please double check restart settings in config.card"
1117	IGCM_debug_Verif_Exit
1118	fi
1119	fi
1120
1121	fi
1122	fi
1123
1124	if [ ${nb_restart_file} -gt 1 ] ; then
1125	j=0 # BASH LINE NOT NEEDED
1126	#BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
1127	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
1128	j4=${j} # BASH LINE NOT NEEDED
1129	if [ X${Buffered} = Xtrue ] ; then
1130	IGCM_sys_GetBuffer ${Path_BUF}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
1131	elif [ X${Archived} = Xtrue ] ; then
1132	IGCM_sys_Get ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
1133	elif [ X${Tared} = Xtrue ] ; then
1134	IGCM_sys_Mv ${comp}_${generic_restart_file_name_in}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
1135	fi
1136	(( j=j+1 )) # BASH LINE NOT NEEDED
1137	done
1138	else
1139	if [ X${Buffered} = Xtrue ] ; then
1140	eval IGCM_sys_GetBuffer \${R_BUF_${comp}_R}/${file_in_Name} ${file_out}
1141	elif [ X${Archived} = Xtrue ] ; then
1142	eval IGCM_sys_Get \${R_OUT_${comp}_R}/${file_in_Name} ${file_out}
1143	elif [ X${Tared} = Xtrue ] ; then
1144	IGCM_sys_Mv ${comp}_${file_in_Name} ${file_out}
1145	fi
1146	fi
1147	done
1148	else
1149	if [ X${FileName0} != XNONE ] ; then
1150	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
1151	else
1152	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
1153	fi
1154	fi
1155	fi
1156	done
1157
1158	NbFiles=$( ls * 2> /dev/null \| wc -l )
1159	if [ ${NbFiles} -gt 0 ] ; then
1160	IGCM_sys_Chmod u+rw *
1161	fi
1162
1163	IGCM_debug_PopStack "IGCM_comp_GetInputRestartFiles"
1164	}
1165
1166	#=======================================================================
1167	function IGCM_comp_GetInputBinaryFiles
1168	{
1169	IGCM_debug_PushStack "IGCM_comp_GetInputBinaryFiles"
1170
1171	# Debug Print :
1172	echo
1173	IGCM_debug_Print 1 "IGCM_comp_GetInputBinaryFiles"
1174	echo
1175
1176	# Clean up previous pass
1177	[ -f ${RUN_DIR}/compiler.txt ] && rm -f ${RUN_DIR}/compiler.txt
1178
1179	typeset comp ExeNameIn ExeNameOut byPass
1180	typeset compilerNmbr compilerUnit compilerFull
1181	byPass=false
1182	for comp in ${config_ListOfComponents[*]} ; do
1183	# Define component
1184
1185	# Copy executable for this component
1186	eval ExeNameIn=\${config_Executable_${comp}[0]}
1187	eval ExeNameOut=\${config_Executable_${comp}[1]}
1188	# Test if missing executable and DRYRUN is set to 0 or 1, then stop!
1189	if [ ${DRYRUN} -le 1 ] && [ X${ExeNameIn} != X\"\" ] ; then
1190	# The executable is set in config.card and is different from ""
1191	# Use eval to expand ExeNameIn if variables are used in the name
1192	eval ExeNameIn=${ExeNameIn}
1193	if [ ! -f ${R_EXE}/${ExeNameIn} ] ; then
1194	IGCM_debug_Exit "IGCM_comp_GetInputBinaryFiles missing executable ${ExeNameIn}"
1195	fi
1196	fi
1197
1198	if [ ${Period} -eq 1 ] && [ -f ${R_EXE}/${ExeNameIn} ] ; then
1199	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
1200	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
1201	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
1202	fi
1203	elif [ -f ${R_EXE}/${ExeNameIn} ] && [ ! -f ${RUN_DIR}/${ExeNameOut} ] ; then
1204	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
1205	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
1206	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
1207	fi
1208	fi
1209
1210	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
1211	# Get the compiler version
1212	compilerFull=$( strings ${RUN_DIR}/${ExeNameOut} \| grep "RTL Message Catalog" \| gawk '{print $6}' \| gawk -F. '{print $1}' )
1213	compilerVersion=$( strings ${RUN_DIR}/${ExeNameOut} \| grep "RTL Message Catalog" \| gawk '{print $6}' \| gawk -F. '{print $1}' )
1214	# Save it
1215	echo $compilerFull >> ${RUN_DIR}/compiler.txt
1216	[ X${compilerFull} = X ] && byPass=true
1217	IGCM_debug_Print 1 "${RUN_DIR}/${ExeNameOut} has been compiled with ${compilerFull}"
1218	IGCM_debug_Print 1 "Compiler is ${compilerVersion}"
1219	fi
1220	done
1221
1222	compilerNmbr=$( cat ${RUN_DIR}/compiler.txt \| wc -l )
1223	compilerUnit=$( cat ${RUN_DIR}/compiler.txt \| sort \| uniq -c )
1224
1225	if ( [ ${compilerNmbr} -ne ${compilerUnit} ] && [ ! X${byPass} = Xtrue ] ); then
1226	IGCM_debug_Exit "Binaries has not been compiled with the same compiler version"
1227	fi
1228
1229
1230	IGCM_debug_PopStack "IGCM_comp_GetInputBinaryFiles"
1231	}
1232
1233	#=======================================================================
1234	function IGCM_comp_PeriodStart
1235	{
1236	IGCM_debug_PushStack "IGCM_comp_PeriodStart"
1237
1238	# Debug Print :
1239	echo
1240	IGCM_debug_Print 1 "IGCM_comp_PeriodStart"
1241	echo
1242
1243	typeset ExeNameIn ExeNameOut
1244	typeset comp compname comptagname
1245	for comp in ${config_ListOfComponents[*]} ; do
1246	# Define component
1247	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
1248	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
1249
1250	# Copy executable for this component
1251	eval ExeNameIn=\${config_Executable_${comp}[0]}
1252	eval ExeNameIn=${ExeNameIn}
1253	eval ExeNameOut=\${config_Executable_${comp}[1]}
1254
1255	# Debug Print
1256	IGCM_debug_Print 3 "PeriodStart ${compname} Driver Function (if any)."
1257	# UPDATE component
1258	${comp}_PeriodStart 2> /dev/null
1259
1260	done
1261
1262	IGCM_debug_PopStack "IGCM_comp_PeriodStart"
1263	}
1264
1265
1266
1267	#=======================================================================
1268	function IGCM_comp_modifyFile
1269	{
1270	#
1271	# syntax: IGCM_comp_modifyFile filein key [value]
1272	#
1273	# For example : IGCM_comp_modifyFile metrics_template.py case_id \'SE_${YEARS}\'
1274	#
1275	# This function is used to replace a pattern in a file for a specific variable.
1276	#
1277	# Arguments:
1278	# - filein : the file in run directory in which the variable should be set
1279	# - key : the variable to modify
1280	# - value : the value to set the key equal to
1281	#
1282	IGCM_debug_PushStack "IGCM_comp_modifyFile"
1283
1284	typeset filein key value pattern
1285
1286	# Set local variables and test the arguments
1287	if [ $# = 3 ] ; then
1288	# Normal case with 3 arguments
1289	filein=$1 ; key=$2 ; value=$3
1290	else
1291	IGCM_debug_Exit "IGCM_comp_modifyFile: Bad number of arguments."
1292	IGCM_debug_PopStack "IGCM_comp_modifyFile"
1293	return
1294	fi
1295	IGCM_debug_Print 1 "Entering IGCM_comp_modifyFile with arguments: ${filein} ${key} ${value}"
1296
1297	# Test if the file exist
1298	if [ ! -f ${filein} ] ; then
1299	IGCM_debug_Exit "IGCM_comp_modifyFile: ${filein} does not exist."
1300	IGCM_debug_PopStack "IGCM_comp_modifyFile"
1301	return
1302	fi
1303
1304	# Read the line with key in the file without the comments
1305	pattern=$( grep "^ ${key} =" ${filein} \| sed -e "s% \!.%%" )
1306
1307	# Verify the existance of the pattern
1308	if [ X"${pattern}" = X ] ; then
1309	# Variable key is not set in filein, stop.
1310	IGCM_debug_Exit "IGCM_comp_modifyFile : Variable ${key} is not set in correct file. It should be set in ${filein}."
1311	IGCM_debug_PopStack "IGCM_comp_modifyFile"
1312	return
1313	fi
1314
1315	# Now change key in filein
1316	#sed -e "s:${pattern}:${key}=${value}:" ${filein} > ${filein}.tmp
1317	sed -e "s:^ ${key} =.*:${key}=${value}:" ${filein} > ${filein}.tmp
1318	IGCM_debug_Print 1 "IGCM_comp_modifyFile: In ${filein} set ${key}=${value}"
1319	\mv ${filein}.tmp ${filein}
1320
1321	IGCM_debug_PopStack "IGCM_comp_modifyFile"
1322	}
1323
1324	#=======================================================================
1325	function IGCM_comp_modifyDefFile
1326	{
1327	#
1328	# syntax: IGCM_comp_modifyDefFile type filein key [value]
1329	#
1330	# For example : IGCM_comp_modifyDefFile blocker run.def day_step 1200
1331	#
1332	# This function is used to modify a parameter file for a specific variable.
1333	# The file must be a ".def" file, i.e. with IOIPSL parameter file syntax.
1334	# This function can be used in the comp.driver files for the components.
1335	#
1336	# Arguments:
1337	# - type : first argument must be blocker, nonblocker or force
1338	# For "blocker" case, the variable must be attributed the keyworld AUTO
1339	# otherwise this function will exit.
1340	# For "nonblocker" case, the user can remove or modify the variable. For
1341	# this case, as long as AUTO is not set, no modification will be done.
1342	# For "force" case, the variable will be modified even if it is not set to AUTO
1343	# - filein : the file in run directory of .def type in which the variable should be set
1344	# - key : the variable to modify
1345	# - value : the value to set the key equal to, optional. If value is not set or if
1346	# value=DEFAULT, then a default value must be given in filein using syntax :
1347	# key= AUTO : DEFAULT=def_value
1348	#
1349	IGCM_debug_PushStack "IGCM_comp_modifyDefFile"
1350
1351	typeset type filein key value
1352	typeset filelist nb_occ modify
1353
1354	# Set local variables and test the arguments
1355	if [ $# = 4 ] ; then
1356	# Normal case with 4 arguments
1357	type=$1 ; filein=$2 ; key=$3 ; value=$4
1358	elif [ $# = 3 ] ; then
1359	# Normal case with 3 arguments
1360	type=$1 ; filein=$2 ; key=$3; value="DEFAULT"
1361	else
1362	IGCM_debug_Exit "IGCM_comp_modifyDefFile: Bad number of arguments."
1363	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1364	return
1365	fi
1366	IGCM_debug_Print 1 "Entering IGCM_comp_modifyDefFile with arguments: ${type} ${filein} ${key} ${value}"
1367
1368	# Test if first argument is correct
1369	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
1370	IGCM_debug_Exit "IGCM_comp_modifyDefFile: Error in first argument must be blocker, nonblocker or force"
1371	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1372	return
1373	fi
1374
1375	# Test if the file exist.
1376	# Exit with error if the file does not exist for the case blocker or force.
1377	# Only return for the case nonblocker.
1378	if [ ! -f ${filein} ] ; then
1379	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
1380	IGCM_debug_Exit "IGCM_comp_modifyDefFile: ${filein} does not exist."
1381	else
1382	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${filein} does not exist. Nothing will be done for this file."
1383	fi
1384	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1385	return
1386	fi
1387
1388	# Define list of files to test using all files with suffix .def (except used*.def)
1389	filelist=$( ls *def \| grep -v used )
1390
1391	# Count number of occurances for the key in all files
1392	nb_occ=$( grep -w ${key} ${filelist} \| grep -v "#" \| wc -l )
1393
1394	# Test if key is set several times
1395	if [ ${nb_occ} -gt 1 ] ; then
1396	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Error in ${filein}: Variable=${key} is set ${nb_occ} times"
1397	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1398	return
1399	fi
1400
1401	# Treatement according to different cases
1402	if [ ${nb_occ} -eq 0 ] && [ ${type} = blocker ] ; then
1403	# Stop if the key is never set and the function is blocker
1404	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Error in ${filein}: Variable=${key} has been removed but this function is blocker. "
1405	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: restore ${filein} for variable ${key}."
1406	elif [ ${nb_occ} -eq 0 ] && [ ${type} = nonblocker ] ; then
1407	# The key is not set but it is a nonblocker call so nothing is done.
1408	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key} is not set in ${filein}. This is a nonblocker call so nothing is done."
1409	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: Default value for ${key} from the model will be used."
1410	modify=no
1411	elif [ $( grep ${key} ${filein} \| grep -v "\#" \|wc -l ) = 0 ] ; then
1412	# Variable key is not set in filein, stop.
1413	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Variable ${key} is not set in correct file. It should be set in ${filein}."
1414	fi
1415
1416	# Check if AUTO is set in the filein on the same line as the key variable
1417	if [ $( grep -w ${key} ${filein} \| grep -v "\#" \| grep AUTO \| wc -l ) = 1 ] ; then
1418	# Modification will be done for all cases
1419	modify=yes
1420	else
1421	# The variable was not set to AUTO
1422	if [ ${type} = blocker ] ; then
1423	# Exit because this is a blocker call
1424	IGCM_debug_Exit "IGCM_comp_modifyDefFile : The variable ${key} cannot be modified. It should be set to AUTO."
1425	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1426	return
1427	elif [ ${type} = nonblocker ] ; then
1428	# Do nothing. Suppose that the user did set the variable correct
1429	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key} is set by the user. Nothing done."
1430	modify=no
1431	elif [ ${type} = force ] ; then
1432	# Force modification
1433	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile : Variabl=${key} was not set to AUTO. Modification will be forced."
1434	modify=yes
1435	fi
1436	fi
1437
1438	# Do the modifcation now
1439	if [ ${modify} = yes ] ; then
1440
1441	# For option DEFAULT, read default value from file.
1442	if [ X"${value}" = XDEFAULT ] \|\| [ X"${value}" = X ] ; then
1443	# Case to set DEFAULT value
1444	# Read default value from filein
1445	value=$( grep -w ${key} ${filein} \| grep -v "\#" \| awk -F"DEFAULT *=" '{print $2}')
1446
1447	if [ X"${value}" = X ] ; then
1448	IGCM_debug_Exit "IGCM_comp_modifyDefFile : The variable ${key} needs a DEFAULT value in ${filein}."
1449	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: The syntax in ${filein} should be:"
1450	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key}=_AUTO_:DEFAULT=def_value"
1451	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1452	return
1453	fi
1454	fi
1455
1456	# Now change key in filein
1457	sed -e "s/^${key}\ =./${key}= ${value}/" ${filein} > ${filein}.tmp
1458	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: In ${filein} set ${key}=${value}"
1459	\mv ${filein}.tmp ${filein}
1460	fi
1461	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1462	}
1463
1464	#=======================================================================
1465	function IGCM_comp_modifyNamelist
1466	{
1467	#
1468	# syntax: IGCM_comp_modifyNamelist type filein key [value]
1469	#
1470	# For example : IGCM_comp_modifyNamelist blocker run.def day_step 1200
1471	#
1472	# This function is used to modify a parameter file for a specific variable.
1473	# The file must be a "namelist" file, i.e. with fortran namelist syntax.
1474	# This function can be used in the comp.driver files for the components.
1475	#
1476	# Arguments:
1477	# - type : first argument must be blocker, nonblocker or force
1478	# For "blocker" case, the variable must be attributed the keyworld AUTO
1479	# otherwise this function will exit.
1480	# For "nonblocker" case, the user can remove or modify the variable. For
1481	# this case, as long as AUTO is not set, no modification will be done.
1482	# For "force" case, the variable will be modified even if it is not set to AUTO
1483	# - filein : the file in run directory of .def type in which the variable should be set
1484	# - key : the variable to modify
1485	# - value : the value to set the key equal to, optional. If value is not set or if
1486	# value=DEFAULT, then a default value must be given in filein using syntax :
1487	# key= AUTO : DEFAULT=def_value
1488	#
1489	IGCM_debug_PushStack "IGCM_comp_modifyNamelist"
1490
1491	typeset type filein key value pattern modify
1492
1493	# Set local variables and test the arguments
1494	if [ $# = 4 ] ; then
1495	# Normal case with 4 arguments
1496	type=$1 ; filein=$2 ; key=$3 ; value=$4
1497	elif [ $# = 3 ] ; then
1498	# Normal case with 3 arguments
1499	type=$1 ; filein=$2 ; key=$3; value="DEFAULT"
1500	else
1501	IGCM_debug_Exit "IGCM_comp_modifyNamelist: Bad number of arguments."
1502	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1503	return
1504	fi
1505	IGCM_debug_Print 1 "Entering IGCM_comp_modifyNamelist with arguments: ${type} ${filein} ${key} ${value}"
1506
1507	# Test if first argument is correct
1508	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
1509	IGCM_debug_Exit "IGCM_comp_modifyNamelist: Error in first argument must be blocker, nonblocker or force"
1510	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1511	return
1512	fi
1513
1514	# Test if the file exist.
1515	# Exit with error if the file does not exist for the case blocker or force.
1516	# Only return for the case nonblocker.
1517	if [ ! -f ${filein} ] ; then
1518	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
1519	IGCM_debug_Exit "IGCM_comp_modifyNamelist: ${filein} does not exist."
1520	else
1521	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${filein} does not exist. Nothing will be done for this file."
1522	fi
1523	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1524	return
1525	fi
1526
1527	# Read the line with key in the file without the comments
1528	pattern=$( grep "^ ${key} =" ${filein} \| sed -e "s% \!.%%" )
1529
1530	# Verify the existance of the pattern
1531	if [ X"$pattern" = X ] ; then
1532	# Variable key is not set in filein, stop.
1533	IGCM_debug_Exit "IGCM_comp_modifyNamelist : Variable ${key} is not set in correct file. It should be set in ${filein}."
1534	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1535	return
1536	fi
1537
1538	# Check if the variable is set to AUTO in the filein
1539	if [ $( echo $pattern \| grep AUTO \| wc -l ) = 1 ] ; then
1540	# Modification will be done for all cases
1541	modify=yes
1542	else
1543	# The variable was not set to AUTO
1544	if [ ${type} = blocker ] ; then
1545	# Exit because this is a blocker call
1546	IGCM_debug_Exit "IGCM_comp_modifyNamelist : The variable ${key} cannot be modified. It should be set to AUTO."
1547	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1548	return
1549	elif [ ${type} = nonblocker ] ; then
1550	# Do nothing. Suppose that the user did set the variable correct
1551	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${key} is set by the user. Nothing done."
1552	modify=no
1553	elif [ ${type} = force ] ; then
1554	# Force modification
1555	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist : Variabl=${key} was not set to AUTO. Modification will be forced."
1556	modify=yes
1557	fi
1558	fi
1559
1560	# Do the modifcation now
1561	if [ ${modify} = yes ] ; then
1562
1563	# For option DEFAULT, read default value from file.
1564	if [ X"${value}" = XDEFAULT ] \|\| [ X"${value}" = X ] ; then
1565	# Case to set DEFAULT value
1566	# Read default value from filein
1567	value=$( echo $pattern \| awk -F"DEFAULT *=" '{print $2}')
1568
1569	if [ X"${value}" = X ] ; then
1570	IGCM_debug_Exit "IGCM_comp_modifyNamelist : The variable ${key} needs a DEFAULT value in ${filein}."
1571	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: The syntax in ${filein} should be:"
1572	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${key}=_AUTO_:DEFAULT=def_value"
1573	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1574	return
1575	fi
1576	fi
1577
1578	# Now change key in filein
1579	sed -e "s/${pattern}/ ${key}=${value}/" ${filein} > ${filein}.tmp
1580	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: In ${filein} set ${key}=${value}"
1581	\mv ${filein}.tmp ${filein}
1582	fi
1583	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1584	}
1585
1586	#=======================================================================
1587	function IGCM_comp_modifyXmlFile
1588	{
1589	#
1590	# syntax: IGCM_comp_modifyXmlFile type filein keyid keyattrib value
1591	#
1592	# For example : IGCM_comp_modifyXmlFile force file_def_orchidee.xml sechiba2 enabled .TRUE.
1593	# or IGCM_comp_modifyXmlFile blocker iodef.xml using_server NONE false
1594	#
1595	# This function is used to modify the value for a specific attribute and variable id.
1596	# The file must be a valid xml file.
1597	# This function can be used in the comp.driver files for the components.
1598	#
1599	# Arguments:
1600	# - type : first argument must be blocker, nonblocker or force.
1601	# For "blocker" case, the variable must be attributed the keyworld AUTO
1602	# otherwise this function will exit.
1603	# For "nonblocker" case, the user can remove or modify the variable. For
1604	# this case, as long as AUTO is not set, no modification will be done.
1605	# For "force" case, the variable will be modified even if it is not set to AUTO
1606	# - filein : the file in run directory of .xml type in which the variable should be set
1607	# - keyid : the variable to modify
1608	# - keyattrib : the attribute name to modify. If NONE, then the variable itself will be modified
1609	# - value : the value to set in the filein
1610	#
1611	IGCM_debug_PushStack "IGCM_comp_modifyXmlFile"
1612
1613	typeset type filein keyid keyattrib value modify
1614
1615	# Set local variables and test the arguments
1616	if [ $# = 5 ] ; then
1617	# Normal case with 4 arguments
1618	type=$1 ; filein=$2 ; keyid=$3 ; keyattrib=$4 ; value=$5
1619	else
1620	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: Bad number of arguments."
1621	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1622	return
1623	fi
1624	IGCM_debug_Print 1 "Entering IGCM_comp_modifyXmlFile with arguments: type=${type} file=${filein}, id=${keyid} attribute=${keyattrib}, value=${value}"
1625
1626	# Test if first argument is correct
1627	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
1628	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: Error in first argument must be blocker, nonblocker or force"
1629	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1630	return
1631	fi
1632
1633	# Test if the file exist.
1634	# Exit with error if the file does not exist for the case blocker or force.
1635	# Only return for the case nonblocker.
1636	if [ ! -f ${filein} ] ; then
1637	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
1638	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: ${filein} does not exist."
1639	else
1640	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile: ${filein} does not exist. Nothing will be done for this file."
1641	fi
1642	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1643	return
1644	fi
1645
1646	# Test if keyid is set in filein. If not exit for case all cases(blocker, force) except nonblocker.
1647	if [ $( grep -w ${keyid} ${filein} \| wc -l ) = 0 ] ; then
1648	if [ ${type} = nonblocker ] ; then
1649	# This is a nonblocker case, print warning but do nothing else
1650	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile: ${keyid} is not set in ${filein}. This is a nonblocker call so nothing is done."
1651	else
1652	# This is a blocker or force case : stop now
1653	IGCM_debug_Exit "IGCM_comp_modifyXmlFile : ${keyid} is not set in the file. Bad syntax of ${filein} file."
1654	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1655	return
1656	fi
1657	fi
1658
1659	# Check if AUTO is set on the same line as keyid and keyattrib
1660	if [ $( grep -w ${keyid} ${filein} \| grep AUTO \| wc -l ) = 1 ] ; then
1661	# Modification will be done
1662	modify=yes
1663	else
1664	if [ ${type} = blocker ] ; then
1665	# Exit, the variable must be set to AUTO
1666	IGCM_debug_Exit "IGCM_comp_modifyXmlFile : blocker function. The ${keyattrib} for ${keyid} must be set to AUTO in ${filein}."
1667	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1668	return
1669	elif [ ${type} = nonblocker ] ; then
1670	# Nothing will be done
1671	IGCM_debug_Print 1 "Nonblocker nothing is done for ${filein}, id=${keyid} and attribute ${keyattrib}"
1672	modify=no
1673	elif [ ${type} = force ] ; then
1674	# Force modification
1675	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile : Attribute=${keyattrib} for id=${keyid} was not set to AUTO. Modification will be forced."
1676	modify=yes
1677	fi
1678	fi
1679
1680	# Do the modifcation now
1681	if [ ${modify} = yes ] ; then
1682	if [ ${keyattrib} = NONE ] ; then
1683	# Case to modify the variable itself
1684	IGCM_debug_Print 1 "Now modify ${filein} for id=${keyid} by setting the variable=${value}"
1685	sed -e "s/\(<[^\"]\"${keyid}\".>\)\([^<]\)\(<[^>]\)/\1${value}\3/" ${filein} > ${filein}.tmp
1686	else
1687	# Check if keyattrib is set on the same line as keyid
1688	if [ $( grep -w ${keyid} ${filein} \| grep ${keyattrib} \| wc -l ) = 1 ] ; then
1689	# Case to modify the attribute value
1690	IGCM_debug_Print 1 "Now modify ${filein} for id=${keyid} by setting attribute to ${keyattrib}=${value}"
1691	sed -e "/id=\"${keyid}\"/s/\(${keyattrib}=\"\)[^\"]*\(\"\)/\1${value}\2/" ${filein} > ${filein}.tmp
1692	else
1693	# Case to add the attribute and its value
1694	IGCM_debug_Print 1 "Now add in ${filein} for id=${keyid} the attribute ${keyattrib} to the value ${value}"
1695	sed -e "/id=\"${keyid}\"/s/\/>/ ${keyattrib}=\"${value}\"\/>/" ${filein} > ${filein}.tmp
1696	fi
1697	fi
1698	\mv ${filein}.tmp ${filein}
1699	fi
1700	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1701	}
1702
1703	#=======================================================================
1704	function IGCM_comp_Update
1705	{
1706	IGCM_debug_PushStack "IGCM_comp_Update"
1707
1708	# Debug Print :
1709	echo
1710	IGCM_debug_Print 1 "IGCM_comp_Update"
1711	echo
1712
1713	typeset comp compname comptagname
1714	for comp in ${config_ListOfComponents[*]} ; do
1715	# Define component
1716	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
1717	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
1718
1719	# Debug Print
1720	IGCM_debug_Print 1 "Update ${compname} Parameter Files."
1721	# UPDATE component
1722	${comp}_Update
1723
1724	# Read TimeSeries information from XML files, prepare TS directories and do modifications in timeseries_def_${compname}.xml
1725	if [ -f timeseries_def_${compname}.xml ]; then
1726	${libIGCM}/libIGCM_post/xios_parser.py tsquery --file timeseries_def_${compname}.xml > ts.temp.${compname}.txt
1727	for line in $( cat ts.temp.${compname}.txt ); do
1728	output_freq=$( echo ${line} \| awk -F "," '{print $1}' \| awk -F "=" '{print $2}' )
1729	id=$( echo ${line} \| awk -F "," '{print $2}' \| awk -F "=" '{print $2}' )
1730	case ${output_freq} in
1731	Y\|y)
1732	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_Y}
1733	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_Y}/${config_UserChoices_JobName}
1734	;;
1735	MO\|mo)
1736	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_M}
1737	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_M}/${config_UserChoices_JobName}
1738	;;
1739	D\|d)
1740	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_D}
1741	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_D}/${config_UserChoices_JobName}
1742	;;
1743	S\|s)
1744	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_H}
1745	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_H}/${config_UserChoices_JobName}
1746	;;
1747	esac
1748	done
1749	fi
1750
1751	# Read TimeSeries information from XML files, prepare CMIP6 TS directories and do modifications in dr2xml_${compname}.xml
1752	if [ -f dr2xml_${compname}.xml ]; then
1753	if ( [ X"$( echo ${config_UserChoices_ExpType} \| grep CMIP6 )" != "X" ] \|\| [ X${config_Post_dr2xmlIPSL} = XTRUE ] ) ; then
1754	eval IGCM_sys_Mkdir \${CMIP6_BUF_${comp}}
1755	eval CMIP6_DIR=\${CMIP6_BUF_${comp}}
1756	# Modify path from dr2xml_{compname}.xml
1757	if [ X${config_Post_dr2xmlIPSL} = XTRUE ]; then
1758	${libIGCM}/libIGCM_post/xios_parser.py -v modifydr2xmlIPSL --newPath ${CMIP6_DIR} --splitLastDate ${EndYear_p1} --JobName ${config_UserChoices_JobName} --ModelName ${config_UserChoices_ModelName} --ModelVersion ${config_UserChoices_LongName} --ExperimentName ${config_UserChoices_ExperimentName} --file dr2xml_${compname}.xml
1759	else
1760	${libIGCM}/libIGCM_post/xios_parser.py -v modifyPath --newPath ${CMIP6_DIR} --file dr2xml_${compname}.xml
1761	fi
1762	# Overwrite the original file
1763	IGCM_sys_Mv modified.dr2xml_${compname}.xml dr2xml_${compname}.xml
1764	fi
1765	fi
1766	done
1767
1768	IGCM_debug_PopStack "IGCM_comp_Update"
1769	}
1770
1771	#=======================================================================
1772	function IGCM_comp_Finalize
1773	{
1774	IGCM_debug_PushStack "IGCM_comp_Finalize"
1775
1776	# Debug Print :
1777	echo
1778	IGCM_debug_Print 1 "IGCM_comp_Finalize"
1779	echo
1780
1781	typeset ListTextName TextName0
1782	typeset comp compname comptagname card ListFilesName FileName0 NbFiles SaveOnArchive
1783	typeset i i_ file_in file_in_ file_out file_out_ file_outin file_outin_ generic_file_name nb_rebuild_file
1784	typeset -Z4 j4 #BASH declare j4
1785	typeset list_file nlist_file
1786	typeset compactoutputs
1787
1788	# Initialize array hosting list of rebuilded files to copy
1789	unset rebuildedActionsList
1790
1791	# Text compacting options
1792	compactoutputs=false
1793	if [ X${JobType} != XRUN ] ; then
1794	compactoutputs=true
1795	elif [ X${config_UserChoices_CompactText} != Xn ] ; then
1796	compactoutputs=true
1797	fi
1798
1799	# Prepare headers for the shell dedicated to offline rebuild
1800	if [ X${AsynchronousRebuild} = Xtrue ] ; then
1801	[ ! -d ${RUN_DIR}/REBUILD_${PeriodDateBegin} ] && IGCM_sys_Mkdir ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1802	if [ ${DRYRUN} -le 1 ] ; then
1803	echo "#!/bin/ksh " > ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1804	echo "function IGCM_FlushRebuild " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1805	echo "{ " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1806	echo "IGCM_debug_PushStack \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1807	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1808	echo "IGCM_debug_Print 1 \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1809	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1810	echo "export R_SAVE=${R_SAVE} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1811	echo "export R_BUFR=${R_BUFR} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1812	echo "export R_OUT_KSH=${R_OUT_KSH} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1813	echo "export R_BUF_KSH=${R_BUF_KSH} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1814	echo "export config_UserChoices_JobName=${config_UserChoices_JobName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1815	echo "export config_UserChoices_SpaceName=${config_UserChoices_SpaceName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1816	fi
1817	fi
1818
1819	for comp in ${config_ListOfComponents[*]} ; do
1820	# Define component
1821	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
1822	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
1823
1824	# Debug Print
1825	IGCM_debug_Print 1 "Finalize ${comp} : ${compname} component."
1826	# FINALIZE component
1827	${comp}_Finalize
1828
1829	card=${SUBMIT_DIR}/COMP/${compname}.card
1830
1831	# Save Output Text files of models
1832	#---------------------------------
1833	IGCM_debug_Print 2 "Save Output Text files for ${comp} : ${compname} component."
1834	IGCM_card_DefineArrayFromOption ${card} OutputText List
1835	ListTextName=${compname}_OutputText_List
1836
1837	eval TextName0=\${${ListTextName}[0]} > /dev/null 2>&1
1838	if [ X${TextName0} != X${NULL_STR} ] ; then
1839	eval NbFiles=\${#${ListTextName}[@]} > /dev/null 2>&1
1840
1841	(( i=0 ))
1842	until [ $i -eq $NbFiles ]; do
1843	eval file_in=\${${ListTextName}[$i]} > /dev/null 2>&1
1844	eval file_out=${PREFIX}_${file_in}
1845
1846	(( i=i+1 ))
1847
1848	unset list_file
1849	#set +A list_file -- $( ls ${file_in}* \| sort 2>/dev/null )
1850	# result for a a1 a10 a2 with file_in=a a a1 a2 a10
1851	set +A list_file -- $( [ -f ${file_in} ] && ls ${file_in} ; for i in $(ls ${file_in}* 2>/dev/null \| sed "s/${file_in}//" \| sort -n) ; do ls ${file_in}$i ; done )
1852	nlist_file=${#list_file[@]}
1853	if [ ${nlist_file} -gt 1 ] ; then
1854	if ( ${compactoutputs} ) ; then
1855	IGCM_debug_Print 2 "Parallelism of Text Output with ${nlist_file} files."
1856	IGCM_debug_Print 2 "Compact files in ${file_out} : " ${list_file[*]}
1857	echo ${list_file[*]} > ${file_out}
1858	echo "" >> ${file_out}
1859
1860	(( i_ = 0 ))
1861	for file in ${list_file[@]} ; do
1862	echo "_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ " >> ${file_out}
1863	echo "\| " ${i_} " " ${file} >> ${file_out}
1864	echo "- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - " >> ${file_out}
1865	cat ${file} \| sed "s/\(.*\)/${i_}\1/" >> ${file_out}
1866	echo "" >> ${file_out}
1867	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
1868	(( i_ = i_ + 1 ))
1869	done
1870	if ( ${ExecutionFail} ) ; then
1871	IGCM_sys_Cp ${file_out} ${SUBMIT_DIR}/Debug
1872	fi
1873
1874	if [ X${Pack} = Xtrue ] ; then
1875	eval IGCM_sys_PutBuffer_Out ${file_out} \${R_BUF_${comp}_D}/${file_out}
1876	else
1877	eval IGCM_sys_Put_Out ${file_out} \${R_OUT_${comp}_D}/${file_out}
1878	fi
1879
1880	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_out}" > /dev/null 2>&1
1881	else
1882	for file in ${list_file[@]} ; do
1883	if ( ${ExecutionFail} ) ; then
1884	IGCM_sys_Cp ${file} ${SUBMIT_DIR}/Debug/${PREFIX}_${file}
1885	fi
1886
1887	if [ X${Pack} = Xtrue ] ; then
1888	eval IGCM_sys_PutBuffer_Out ${file} \${R_BUF_${comp}_D}/${PREFIX}_${file}
1889	else
1890	eval IGCM_sys_Put_Out ${file} \${R_OUT_${comp}_D}/${PREFIX}_${file}
1891	fi
1892
1893	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
1894	done
1895	fi
1896	else
1897	if ( [ -f ${file_in}_0000 ] \|\| [ -f ${file_in}0 ] ) ; then
1898	eval IGCM_sys_Mv ${file_in}* ${file_in}
1899	fi
1900
1901	if ( ${ExecutionFail} ) ; then
1902	IGCM_sys_Cp ${file_in} ${SUBMIT_DIR}/Debug/${file_out}
1903	fi
1904
1905	if [ X${Pack} = Xtrue ] ; then
1906	eval IGCM_sys_PutBuffer_Out ${file_in} \${R_BUF_${comp}_D}/${file_out}
1907	else
1908	eval IGCM_sys_Put_Out ${file_in} \${R_OUT_${comp}_D}/${file_out}
1909	fi
1910	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
1911	fi
1912	done
1913	fi
1914
1915	# Save Restarts files
1916	#--------------------
1917	IGCM_debug_Print 2 "Save Restart files for ${comp} : ${compname} component."
1918	IGCM_card_DefineArrayFromOption ${card} RestartFiles List
1919	ListFilesName=${compname}_RestartFiles_List
1920	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
1921
1922	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
1923	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
1924	(( i=0 ))
1925	until [ $i -ge $NbFiles ]; do
1926	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
1927	eval file_in=${file_in_}
1928
1929	(( i_ = i+1 ))
1930	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1931	eval file_out=${file_out_}
1932
1933	(( i_ = i+2 ))
1934	eval file_outin_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1935	eval file_outin=${file_outin_}
1936
1937	(( i_ = i+3 ))
1938	eval is_opt=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1939	if [ X${is_opt} = XOPTIONAL ] ; then
1940	echo ${file_in} is optional
1941	(( i=i+4 ))
1942	else
1943	is_opt=""
1944	echo ${file_in} is mandatory
1945	(( i=i+3 ))
1946	fi
1947
1948	generic_restart_file_name_in=$( basename ${file_in} .nc )
1949	generic_restart_file_name_out=$( basename ${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out} .nc )
1950	generic_restart_file_name_outin=$( basename ${file_outin} .nc )
1951
1952	nb_restart_file=$( ls ${generic_restart_file_name_in}_????.nc 2>/dev/null \| wc -l )
1953	if [ ${nb_restart_file} -gt 1 ] ; then
1954	IGCM_sys_rebuild_nemo ${generic_restart_file_name_in} ${nb_restart_file}
1955	IGCM_sys_Rm ${generic_restart_file_name_in}_????.nc
1956	if [ X${Pack} = Xtrue ] ; then
1957	eval IGCM_sys_PutBuffer_Rest ${file_in} \${R_BUF_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out} ${is_opt}
1958	else
1959	eval IGCM_sys_Put_Rest ${file_in} \${R_OUT_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out} ${is_opt}
1960	fi
1961	if [ -f ${file_in} ] ; then
1962	if [ ! ${file_in} = ${file_outin} ] ; then
1963	if ( ${ExitFlag} ) ; then
1964	echo "IGCM_sys_Mv ${file_in} ${file_outin} not executed."
1965	else
1966	IGCM_sys_Mv ${file_in} ${file_outin}
1967	fi
1968	fi
1969	else
1970	# This is the case where the restart file no not exist.
1971	# It has already been checked if the model should stop for this case.
1972	IGCM_debug_Print 1 "Restart file does not exist, no move in RUN_DIR done : ${file_in}"
1973	fi
1974	else
1975	if [ X${Pack} = Xtrue ] ; then
1976	eval IGCM_sys_PutBuffer_Rest ${file_in} \${R_BUF_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out} ${is_opt}
1977	else
1978	eval IGCM_sys_Put_Rest ${file_in} \${R_OUT_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out} ${is_opt}
1979	fi
1980
1981	if [ -f ${file_in} ] ; then
1982	if [ ! ${file_in} = ${file_outin} ] ; then
1983	if ( ${ExitFlag} ) ; then
1984	echo "IGCM_sys_Mv ${file_in} ${file_outin} not executed."
1985	else
1986	IGCM_sys_Mv ${file_in} ${file_outin}
1987	fi
1988	fi
1989	else
1990	# This is the case where the restart file no not exist.
1991	# It has already been checked if the model should stop for this case.
1992	IGCM_debug_Print 1 "Restart file does not exist, no move in RUN_DIR done : ${file_in}"
1993	fi
1994	fi
1995
1996	done
1997	else
1998	if [ X${FileName0} != XNONE ] ; then
1999	IGCM_debug_Exit "IGCM_comp_Finalize : No file in restart list for ${compname}."
2000	else
2001	IGCM_debug_Print 1 "IGCM_comp_Finalize : NONE specified in Restart List ${compname}."
2002	fi
2003	fi
2004
2005	# Save Output files
2006	#------------------
2007	IGCM_debug_Print 2 "Save Output files for ${comp} : ${compname} component."
2008	IGCM_card_DefineArrayFromOption ${card} OutputFiles List
2009	ListFilesName=${compname}_OutputFiles_List
2010	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
2011
2012	if [ X${FileName0} != X${NULL_STR} ] ; then
2013	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
2014
2015	(( i=0 ))
2016	until [ $i -ge $NbFiles ]; do
2017	SaveOnArchive=true
2018	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
2019	eval file_in=${file_in_}
2020	(( i_ = i+1 ))
2021	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
2022	eval file_out=${file_out_}
2023	#
2024	# Override file_out path remplacing R_SAVE by R_BUFR
2025	#
2026	if [ X${Pack} = Xtrue ] ; then
2027	file_out=$( echo $file_out \| sed "s:^$R_SAVE:$R_BUFR:" )
2028	fi
2029	#
2030	# Not necessarily the best option. /!\ Potential side effects /!\
2031	#
2032	(( i_ = i+2 ))
2033	eval flag_post=\${${ListFilesName}[$i_]} > /dev/null 2>&1
2034	#
2035	generic_file_name=$( basename ${file_in} .nc )
2036	nb_rebuild_file=$( ls \| grep "^${generic_file_name}_[0-9]*.nc" \| wc -l )
2037	#
2038	if ( [ ${nb_rebuild_file} -eq 1 ] && [ -f ${generic_file_name}_0000.nc ] ) ; then
2039	IGCM_debug_Print 2 "Parallelism with 1 file. Rebuilding ${file_in} not needed"
2040	IGCM_sys_Mv ${generic_file_name}_0000.nc ${file_in}
2041	elif [ ${nb_rebuild_file} -gt 1 ] ; then
2042	IGCM_debug_Print 2 "Parallelism detected and rebuilding ${file_in} is needed"
2043	if [ X${AsynchronousRebuild} = Xfalse ] ; then
2044	IGCM_debug_Print 2 "Rebuilding ${file_in} online"
2045	#
2046	# for output.abort file, let use rebuild_NEMO : 13s instead of 20 mn.
2047	if [ ${file_in} = output.abort.nc ] ; then
2048	IGCM_sys_rebuild_nemo ${generic_file_name} ${nb_rebuild_file} "nc" ${generic_file_name}_[0-9]*.nc
2049	else
2050	IGCM_sys_rebuild ${file_in} ${generic_file_name}_????.nc
2051	fi
2052	else
2053	IGCM_debug_Print 2 "Preparing offline rebuild for ${file_in}"
2054	IGCM_sys_Mv ${generic_file_name}_????.nc ${RUN_DIR}/REBUILD_${PeriodDateBegin}
2055
2056	# Prepare the shell dedicated to offline rebuild
2057	if [ $DRYRUN -le 1 ]; then
2058	if [ ${file_in} = histstn.nc ] ; then
2059	echo "IGCM_sys_rebuild_station ${file_in} ${generic_file_name}_*.nc" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2060	else
2061	echo "IGCM_sys_rebuild ${file_in} ${generic_file_name}_[0-9]*.nc" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2062	fi
2063	echo "IGCM_debug_Verif_Exit" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2064	fi
2065	#
2066	# Load Patch we need to apply and apply
2067	if [ $DRYRUN -le 1 ]; then
2068	if [ X$( eval echo \${${compname}_${flag_post}_Patches[0]} ) != X${NULL_STR} ]; then
2069	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ) ; do
2070	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2071	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2072	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2073	done
2074	fi
2075	fi
2076	#
2077	if [ $DRYRUN -le 1 ]; then
2078	if [ X${Pack} = Xtrue ] ; then
2079	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_sys_PutBuffer_Out ${file_in} ${file_out}"
2080	else
2081	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_sys_Put_Out ${file_in} ${file_out}"
2082	fi
2083	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_debug_Verif_Exit"
2084	rebuildedActionsList[${#rebuildedActionsList[]}]="IGCM_sys_Rm ${generic_file_name}_[0-9].nc"
2085	fi
2086	SaveOnArchive=false
2087	fi
2088	fi
2089	#
2090	if [ ${SaveOnArchive} = true ] ; then
2091	#
2092	# Rebuild has been done online or it was not needed
2093	#
2094	# If we need to apply a patch we use TMP DIRECTORY before ARCHIVING if asynchronous rebuild is on
2095	#
2096	thereisapatch=$( eval echo \${${compname}_${flag_post}_Patches[0]} )
2097	if ( [ ! X${thereisapatch} = X${NULL_STR} ] && [ ! X${thereisapatch} = X ] && [ X${AsynchronousRebuild} = Xtrue ] && [ -f ${file_in} ] ) ; then
2098	IGCM_sys_Mv ${file_in} ${RUN_DIR}/REBUILD_${PeriodDateBegin}
2099	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=REBUILD_${PeriodDateBegin}/${file_in} > /dev/null 2>&1
2100	#
2101	if [ $DRYRUN -le 1 ]; then
2102	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ) ; do
2103	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2104	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2105	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2106	done
2107	#
2108	if [ X${Pack} = Xtrue ] ; then
2109	echo "IGCM_sys_PutBuffer_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2110	else
2111	echo "IGCM_sys_Put_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2112	fi
2113	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2114	#
2115	fi
2116	else
2117	#
2118	# No Patch, No Asynchronous rebuild, online rebuild has been done or was not needed
2119	#
2120	if [ X${Pack} = Xtrue ] ; then
2121	IGCM_sys_PutBuffer_Out ${file_in} ${file_out}
2122	else
2123	IGCM_sys_Put_Out ${file_in} ${file_out}
2124	fi
2125	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
2126	if [ ${nb_rebuild_file} -gt 1 ] ; then
2127	for DelFile in $( ls \| grep "${generic_file_name}[_0-9]*.nc" ) ; do
2128	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=${DelFile} > /dev/null 2>&1
2129	done
2130	fi
2131	fi
2132	fi
2133	((i_ = i_ +1))
2134	eval Testvar_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
2135	eval Testvar=${Testvar_}
2136	if [[ ${Testvar} =~ [0-9][DMY]$ ]] ; then
2137	((i = i+4))
2138	else
2139	(( i=i+3 ))
2140	fi
2141	done
2142	fi
2143	echo
2144	done
2145	# Append the sync call and the copy sequence to the IGCM_FlushRebuild function if needed
2146	if [ ${#rebuildedActionsList[*]} -ne 0 ] ; then
2147	echo "IGCM_sys_sync " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2148	i=0
2149	until [ ${i} -ge ${#rebuildedActionsList[*]} ]; do
2150	echo ${rebuildedActionsList[$i]} >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2151	(( i=i+1 ))
2152	done
2153	fi
2154	IGCM_debug_PopStack "IGCM_comp_Finalize"
2155	}

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